Certainly worth considering, Douglas, but IBD doesn't tend to be exercise-provoked. Also the OP makes no mention of cramping, blood, mucous, mouth ulcers etc. However, it could be an atypical presentation and in all likelihood a Gastroenterologist would be the first expert a GP would refer to in this instance, to rule out a GI cause. If a GI cause is ruled out and other extensive tests fail to identify a cause, the Gastros often send the patients to the Immunologists.
Funnily enough I worked for a Consultant Gastroenterologist (who was Clinical Lead for IBD) until Feb this year.